CBM2 Plastics Engineering for Microfluidics and Nanofluidics

Plastics Engineering cover
  • CBM2 has been involved in building and using polymer-based microfluidic systems since 1995 for a variety of biomedical applications.
  • We have generated a significant amount of know-how and infrastructure to develop and design highly innovative devices.
  • CBM2’s multi-institutional format, with resources available at Center-associated infrastructure situated at KU-L, UNC, and LSU, facilitates innovation.
  • We recently expanded our already extensive resources for building and using nanofluidic devices using plastics as the substrate material.
    • This is a very unique capability of CBM2.
    • We have the necessary tools to build even sub-10 nm structures in plastics.
    • Structures can be sealed with cover plates with high process yield rates.
  • Our team has know-how in terms of assembly and functionalization of devices,
  • Selected applications of our devices for various biomedical applications.

Micro- and nanofabrication infrastructure

Our plastic fabrication infrastructure is located at three sites as noted above and possesses tools for rapid prototyping, microfabrication, nanofabrication, and metrology.

Rapid Prototyping

High precision mill
High precision mill
Laser writing machine
Laser writing machine

We have two machines to do rapid prototyping of microfluidic devices in plastics. These include a high precision micromill (KU, LSU, and UNC) and a laser milling system using both an excimer laser (UNC) and a CO2 laser (KU). The milling machine can spin carbide bits as small as 25 µm by spinning at extremely high revolution rates. The mill can be used to write structures directly into plastics or into soft metals such as brass, which can be subsequently used a molding tools for hot embossing or injection molding. Channel widths as small as 25 µm can be fabricated with aspect ratios of 4:1 and side wall roughness ~300 nm.

Laser machining, in particular laser ablation, can directly write structures into plastics with the smallest feature size of 5 µm and an aspect ratio of 5:1. The laser sources are either a KrF laser (248 nm) or an ArF laser (193 nm). The selection of laser type is predicated on the type of material serving as the substrate. For example, polycarbonate can be used with the KrF laser, which cyclic olefin copolymers or PMMA can use the ArF laser.

Micro/nanofabrication (replication):

HEX03 hot embosser

NIL machine

Injection molding machine

We have developed world-class fabrication (replication) capabilities of plastic devices using a variety of techniques such as hot embossing, imprinting, nanoimprint lithography (NIL), and injection molding (also injection compression molding). In addition, we have great working relationships with several commercial foundries such as Stratec.

production of_plastic chips stratec
Typically replication-based technologies, no matter what the scale (micro or nano), require molding tools, and CBM2 has a variety of methods it has perfected to build masters for replication production of final devices. For example, we can make molding tools for hot embossing and injection molding using high precision Micromilling, and if feature sizes demand (<10 µm with aspect ratios >5:1), we can use a combination of lithography and electroplating (LiGA) to build the desired molding tools. For nanoscale structures, we use the nano-patterning capabilities we have access to, which consists of focused ion beam milling to make nanostructures and conventional optical lithography to build microstructures. This is followed by using UV-NIL to make resin stamps that can go into our NIL machines to produce final parts in plastics via thermal NIL. The Center is fortified by the extensive resources found in our cleanrooms, such as KUNF at the University of Kansas, CHANL at the University of North Carolina, and CAMD at Louisiana State University (please see Fabrication Facilities in this website for additional information)

Here are the replication tools we possess within the Center:

  • Jenoptik HEX02 (LSU) and HEX03 (KU and UNC)
  • PHI Precision Press (KU)
  • Wabash Press (KU)
  • Obducat NIL machine (LSU)
  • Nanonex NIL machine (KU)
  • Arburg injection molding machine (also does injection compression molding) (KU)


Rapid Scanning Profiler
Rapid Scanning Profiler
Atomic Force Microscope
Atomic Force Microscope

We have within the Center, several tools for metrology across many different length scales. For example, we have several AFMs for determining replication fidelity in nanofluidic devices including a new Shimadzu scanning probe microscope and a Keyence rapid scanning confocal microscope for performing non-contact profilometry. The Keyence uses a violet laser that allows for depth profiling around 100 nm.

Device assembly and functionalization

cover page--final_dimensions
LOC back cover for nanofluidic bonding
Bonding Device
Thermally fusion bonded device
ozone chamber
UV/O2 Chamber used to activate polymers

We have developed assembly techniques, which consist of bonding a cover plate to a patterned microfluidic or nanofluidic substrate, using thermal fusion bonding. In the case of microfluidic devices, we take a cover plate made of the same material as the substrate, and heat both pieces to near their glass transition temperature (Tg), which can be done in a convection oven with the two pieces clamped together or in a precision press with heated platens, and apply a certain amount of pressure to the plastics. This results in minimal deformation of the underlying structures as noted in the picture above, which shows microchannels that are 25 µm wide and 150 µm deep. The process yield rate of using this technique is >95%.

In the case of nanofluidic devices, we use a hybrid-based approach, which consists of thermal fusion bonding a high Tg substrate to a low Tg cover plate. When using bonding temperature close to the Tg of the cover plate, we can generate process yield rates >90% even for devices containing nanostructures as small as 10 nm.

Following device assembly, we can activate the surface of the plastic to both make it more hydrophilic (i.e., wettable) and create functional scaffolds (surface-confined carboxylic acids) for the covalent attachment of biologics, such as recognition elements or enzymes, using standard EDC/NHS coupling chemistry. This can be accomplished by exposing the device to UV/O3 radiation using a very simple instrument.

Applications of plastic devices

cover page--final_dimensions

in-plane nanopore 43_nm

in-plane nanopore 10_nm
Tailoring in-plane pore size

integrated system 2020
Modular fluidic system in-plane nanopore 10_nm
Two in-plane pores

We have placed in the public domain a number of publications that highlight our ability to not only fabricate microfluidic and nanofluidic devices, but also use them in compelling biomedical applications. For example, we have used our plastic-based microfluidic devices for ultra-fast PCRs, electrophoresis, electrochromatography, solid-phase extractions, ligase detection reactions for the detection of point mutations, micro-optics, solid-phase bioreactors, and the isolation of liquid biopsy markers (see the Liquid Biopsy section in this website for more information on this topical area).

In terms of nanofluidics, which is a relatively new area for us, we have leveraged our ability to build functional devices with sub-100 nm structures for such applications of electrophoresis analysis of both small and large molecules, stretching DNA to detect chemotherapy-induced damage, and a new application we are developing which involves a single-molecule DNA/RNA sequencing platform (being co-developed by our commercial partner, Sunflower Genomics, Inc.).

We have also used many of the discoveries emanating from the Center to develop integrated and modular mixed-scale systems that can perform multi-step assays in a fully automated fashion. The integrated system idea we are pursuing is a modular one, in which task-specific modules are connected to a fluidic motherboard. The connections of the modules to the motherboard is achieved using superhydrophobic seals. The modules can be used as standalone units as well. We are adopting a universal fluidic motherboard approach so that modules can be easily interchanged to change the function of the system.

Representative Publications

  1. Microelectromechanical Systems (MEMS) Fabricated in Polymeric Materials: Applications in Chemistry and Life Sciences. S.A. Soper, S.M. Ford, S. Qi, R.L. McCarley, K. Kelly and M.C. Murphy, Anal. Chem. 72 (2000) 642A-651A. This article was featured on the cover of Analytical Chemistry, vol. 72, 2000.
  2. Interfacing a Polymer-based Micromachined Device to a Nanoelectrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometer, Z. Meng, S. Qi, S.A. Soper, P.A. Limbach, Anal. Chem. 73 (2001) 1286-1291.
  3. Hot Embossing High-Aspect-Ratio Microstructures in Poly(methyl methacrylate) for Constructing Microfluidic Devices with Integrated Components, S. Qi, S. Ford, X. Liu, J. Barrows, G. Thomas, K. Kelly, A. McCandless, K. Lian, J. Goettert, S.A. Soper, Lab Chip 2 (2002) 88-95.
  4. Contact Conductivity Detection in PMMA-Based Microfluidic Devices for the Transduction of Mono- and Polyionic Molecules, M. Galloway, W. Stryjewski, D. Patterson, A. Henry, R.L. McCarley and S.A. Soper, Anal. Chem. 74 (2002) 2407-2415.
  5. Surface Modification of Polymer-based Microfluidic Devices. S.A. Soper, M. Galloway, A.C. Henry, B. Vaidya, Y. Wang and R.L. McCarley, Anal. Chim. Acta, 470 (2002), 87-99.
  6. BioMEMS using Electrophoresis for the Analysis of Genetic Mutations, G.A. Thomas, H.D. Farquar, S. Sutton, R.P. Hammer, S.A. Soper, Expert Rev. Molc. Diagn. 2 (2002) 429-447.
  7. Surface Modification and Characterization of Microfabricated Poly(carbonante) Devices: Manipulation of Electroosmotic Flow.  B. Vaidya, S.A. Soper and R.L. McCarley, Analyst 127 (2002) 1289-1292.
  8. Microarrays Assembled in Microfluidic Chips Fabricated form Poly(methylmethacrylate) for the Detection of Low Abundant Mutations, Y. Wang, B. Vaidya, Y.-Wei Cheng, F. Barany, H.D. Farquar, R.P. Hammer and S.A. Soper, Anal. Chem. 75 (2003) 1130-1140.
  9. Solid Phase Reversible Immobilization in Microfluidic Chips for the Purification of Dye-Labeled DNA Sequencing Fragment, Y. Xu, B. Vaidya, R.L. McCarley and S.A. Soper, Anal. Chem. 75 (2003) 2975-2984.
  10. Rapid PCR in a Continuous Flow Device, M. Hashimoto, P. Chen, M.W. Mitchell, D.E. Nikitopoulos, S.A. Soper and M.C. Murphy, Lab Chip 4 (2004) 638-645.
  11. Electrokinetically-synchronized Polymerase Chain Reaction Microchip Fabricated in Polycarbonante, J. Chen, H. Chen, M. Wabuyele, D. Patterson, M. Hupert, H. Shadpour, S.A. Soper, Anal. Chem. 77 (2005) 658-666.
  12. Rapid Patterning of DNA Microarrays on Photo-Activated PMMA for the Detection of Low Abundant Point Mutations in K-ras Genes, C. Situma, Y. Wang, M. Hupert, F. Barany, R.L. McCarley and S.A. Soper, Anal. Biochem. 340 (2005) 123-135.
  13. Photochemically Patterned Poly(methyl methacrylate) Surfaces Used in the Fabrication of Microanalytical Devices, S. Wei, B. Vaidya, A.B. Patel, S.A. Soper and R.L. McCarley, J. Phys. Chem. B 109 (2005) 16988-16996.
  14. Investigation of the Physico-Chemical Properties of Various Polymers for Microchip Electrophoresis Applications, H. Shadpour, H. Musyimi, J. Chen and S.A. Soper, J. Chromatogr. A 1111 (2006) 238-251.
  15. Polymerase Chain Reaction/Ligase Detection Reaction/Hybridization Assays Using Flow-Through Microfluidic Devices for the Detection of Low Abundant DNA Point Mutations, M. Hashimoto, F. Barany and S.A. Soper, Biosen. & Bioelectr. 21 (2006) 1915-1923.
  16. Two-Dimensional Separation of Proteins using Poly(methyl methacrylate) Microchips, H. Shadpour and S.A. Soper, Anal. Chem. 78 (2006) 3519-3527. This article was featured in AC Research Highlights and J. Proteome Res. (2006).
  17. Micro-milling of polymers for microfluidic applications, M. Hupert, H. Shadpour, D. Nikitopoulos and S.A. Soper, Microfluidics and Nanofluidics 3 (2007) 1-11.
  18. Surface Modification of PMMA Microfluidic Devices for High-Resolution Separations of Single-Stranded DNA, S. Llopis, J. Osiri and S.A. Soper, Electrophoresis 28 (2007) 984-993.
  19. Fabrication of Large Area Mold Inserts for Replication of Polymer Microparts, D. Park, M. Witek, M. Hupert, R.L. McCarley, S.A. Soper and M.C. Murphy, Biomed. Microdev. 9 (2007).
  20. Free-standing, Erect Ultra-high-aspect-ratio Polymer Nanopillar and Nanotube Ensembles, G. Chen, S.A. Soper and R.L. McCarley, Langmuir 23 (2007) 11777-11781.
  21. Polymer Microfluidic Chips with Integrated Waveguides for Reading Microarrays, F. Xu, P. Datta, H. Wang, S. Gurung, M. Hashimoto, S. Wei, J. Goettert, R. L. McCarley, S. A. Soper, Anal. Chem. 79 (2007) 9007-9013.
  22. Capture and Enumeration of Circulating Tumor Cells from Peripheral Blood using Microfluidics, A.A. Adams, P. Okagbare, J. Feng, R.L. McCarley, M.C. Murphy and S.A. Soper, J. Am. Chem. Soc. 130 (2008) 8633-8641.
  23. 96 Well Microfluidic Titer Plate for High Throughput Purification of DNA and RNA, M. Witek, D. Park, M. Hupert, R.L. McCarley, M.C. Murphy and S.A. Soper, Anal. Chem. 80 (2008) 3483-3491.
  24. Microfluidics with MALDI-MS Analysis for Proteomics. J. Lee, S.A. Soper, K.K. Murray, Anal. Chim. Acta 649 (2009) 180-190.
  25. Highly Efficient Capture and Enumeration of Low Abundance Prostate Cancer Cells Using Prostate-Specific Membrane Antigen Aptamers Immobilized to a Polymeric Microfluidic Device. U. Dharmasiri, S. Balamurugan, R.L. McCarley, D. Spivak and S.A. Soper, Electrophoresis 30 (2009) 3289-3300.
  26. Enrichment and Detection of Escherichia coli O157:H7 from Water Samples Using an Antibody Modified Microfluidic Chip, U. Dharmasiri, M. A. Witek, A. A. Adams, J. K. Osiri, M. L. Hupert, T. S. Bianchi, D. L. Roelke, and S. A. Soper, Anal. Chem. 82 (2010) 2844-2849.
  27. Simple Fabrication Methods for Producing 1D Nanoslits in Thermoplastics and the Transport Dynamics of Double-Stranded DNA through these Slits, R. Chantiwas, M. Hupert, S. Park, P. Datta, J. Goettert, Y.-K. Cho, and S. A. Soper, Lab on a Chip 10 (2010) 3255-3264.
  28. Flexible Fabrication and Applications of Polymer Nanochannels and Nanoslits, R. Chantiwas, S. Park, S.A. Soper, B.L. Kim, S. Takayama, V. Sunkara, H. Hwang, Y.K. Cho, Chem. Soc. Rev. 40 (2011) 3677-3702.
  29. High-throughput Selection, Enumeration, Electrokinetic Manipulation, and Molecular Profiling of Low-Abundance Circulating Tumor Cells. U. Dharmisiri, S.A. Soper, Anal. Chem. 83 (2011) 2301-2309.
  30. Surface Modification of Droplet Polymeric Microfluidic Devices for the Stable and Continuous Generation of Aqueous Droplets, S. Balamurugan, N. Kim, W. Lee, D.A. Spivak, D. Nikitopoulos, R.L. McCarley, and S.A. Soper, Langmuir 27 (2011) 7949-7957.
  31. Complete plastic nanofluidic devices for DNA analysis via direct imprinting with polymer stamps, J. Wu, R. Chantiwas, A. Amirsadeghi, S.A. Soper, and S. Park, Lab on a Chip 11 (2011) 2984-2989.
  32. Fully Integrated Thermoplastic Genosensor for the Highly Sensitive Detection and Identification of Multi-Drug-Resistant Tuberculosis, H. Wang, H.W. Chen, M.L. Hupert, P.C. Chen, P. Datta, T.L. Pittman, J. Goettert, M.C. Murphy, D. Williams, F. Barany, S.A. Soper, Angewandte Chemie, Int. Ed. 51 (2012) 4349-4353.
  33. Modular Microfluidic System Fabricated in Thermoplastics for the Strain-Specific Detection of Bacterial Pathogens, H.W. Chen, H. Wang, M. Hupert, S.A. Soper, Lab Chip 12 (2012) 3348-3355.
  34. Influence of material transition and interfacial area changes on flow and concentration in electro-osmosis flows, S.D. Rani, B.-Y. You, S.A. Soper, M.C. Murphy, D.E. Nikitopoulos, Anal. Chimica Acta 770 (2013) 103-110.
  35. Influence of material transition and interfacial area changes on flow and concentration in electro-osmosis flows, S.D. Rani, B.-Y. You, S.A. Soper, M.C. Murphy, D.E. Nikitopoulos, Anal. Chimica Acta 770 (2013) 103-110.
  36. Parallel affinity-based isolation of leukocyte subsets using microfluidics: Applications for stroke diagnosis, S.R. Pullagurla, M.A. Witek, J.M. Jackson, M.M. Lindell, M.L. Hupert, I.V. Nesterova, A.E. Baird and S.A. Soper, Anal. Chem. 86 (2014) 4058-4065.
  37. Immobilization of lambda exonuclease onto polymer micropillar arrays for the solid-phase digestion of dsDNAs, N.J. Oliver-Calixte, F.I. Uba, K.N. Battle, K.M.W. Ratnayake and S.A. Soper, Anal. Chem. 86 (2014) 4447-4454.
  38. Investigation of surface charge and electroosmostic flow in polymer nanoslits and nanochannels, F.I. Uba, S.R. Pullagurla, N. Sirasunthorn, J. Wu, S. Park, R. Chantiwas, Y. Cho, H. Shin and S.A. Soper, Analyst 140 (2015) 113-126.
  39. Capture and Enzymatic Release of Circulating Tumor Cells, Soumya Nair, Joshua Jackson, Maggie Witek, V. Bae-Jump, P.A. Gehrig, W.Z. Wysham, P.M. Armistead, P. Voorhees and S.A. Soper, Chemical Communications 51 (2015) 3266-3269.
  40. Characterizing Surface Functional Group Density for O2 Plasma and UV/O3 Activated Thermoplastics using Superresolution Microscopy, C.E. O’Neil, J.M. Jackson, S.H. Shim and S.A. Soper, Analytical Chemistry 88 (2016) 3686-3696.
  41. Characterization of Activated Cyclic Olefin Copolymer: Effects of Ethylene/Norbornene Content on the Physiochemical Properties. C.E. O’Neil, S. Taylor, K. Ratnayake, S. Pullagurla, V. Singh and S.A. Soper, Analyst 141 (2016) 6521-6532.
  42. Thermoplastic Nanofluidic Devices for Biomedical Applications, K. Weerakoon-Ratnayake, C.E. O’Neil, F.I. Uba and S.A. Soper, Lab on a Chip, 17 (2017) 362-381.
  43. Materials and Microfluidics: Enabling the Efficient Isolation and Analysis of Circulating Tumour Cells, J.M. Jackson, M. Witek, J. Kamande and S.A. Soper, Chem. Soc. Rev. 46 (2017) 4245-4280.
  44. Isolation of Circulating Plasma Cells from Blood of Patients Diagnosed with Clonal Plasma Cell Disorder using Cell Selection Microfluidics, S.A. Soper, J. Kamande, M. Lindell, M. Witek and P. Voorhees, Integr. Biol. 10 (2018) 82 – 91.
  45. Electrokinetic Transport Properties of Deoxynucleotide Monophosphates (dNMPs) through Thermoplastic Nanochannels, C. O'Neil, C.A. Amarasekara, K.M. Weerakoon-Ratnayake, B. Gross, Z. Jia, V. Singh, S. Park, S.A. Soper, Anal. Chim. Acta, 1027 (2018) 67-75.
  46. Open tubular nanoelectrochromatography (OT — NEC): gel — free separation of single stranded DNAs (ssDNAs) in thermoplastic nanochannels, C. A. Amarasekara, U. S. Athapattu, C. Rathnayaka, J. Choi, S. Park, and Steven A. Soper, Electrophoresis 41 (2020) doi.org/10.1002/elps.202000109.
  47. Micro-Coulter Counter for Enumerating Enriched Circulating Tumor Cells, K. Ratnayaka, M.J. Hu, K. Cong, and S. A. Soper, Analyst (2020).